P01 figures
Ryan Sheridan
2024-12-02
Meta-analysis
The response to antigen, virus, or mRNA vaccine uptake was compared across samples, the general approach:
- Differentially expressed genes were identified for Ag-high vs -low (or virus, mRNA vaccine, etc.) LECs for each sample. LECs were not divided into subsets.
- PCA was performed using the fold change in expression for DEGs (Ag-high / Ag-low), the top genes from PC1 were identified
- A random effects model was used to identify genes that show the most consistent response across samples.
- PCA plot showing similarity of the Ag/virus/vaccine response across samples
- The top genes from PC1 were clustered based on fold change in expression
- Gene ontology terms are shown for each gene cluster from B.
- The top genes with the most consistent response across samples were clustered as in B.
- Gene ontology terms are shown for each gene cluster from D.
Endocytic receptors
Project 3 will use LYTACs and EndoTags to direct antigen into specific endocytic compartments. Expression of relevant receptors is shown below.
M6pr
Sort1
Tfrc
Igf2r
Session info
## R version 4.3.1 (2023-06-16)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.5 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=en_US.UTF-8
## [9] LC_ADDRESS=en_US.UTF-8 LC_TELEPHONE=en_US.UTF-8
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=en_US.UTF-8
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## time zone: America/Denver
## tzcode source: system (glibc)
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## attached base packages:
## [1] tools stats4 grid stats graphics grDevices utils
## [8] datasets methods base
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## other attached packages:
## [1] sp_2.1-0 sf_1.0-16
## [3] SpatialOmicsOverlay_1.0.0 umap_0.2.10.0
## [5] GeoMxWorkflows_1.6.0 GeomxTools_3.4.0
## [7] NanoStringNCTools_1.8.0 cli_3.6.1
## [9] devtools_2.4.5 usethis_2.2.2
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